Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Continued colonization of the human genome by mitochondrial DNA.

  PMID 15361937 · PMC515365 · PLoS biology · 2004 · 7 claims · 6 setups

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  NUMT insertion into nuclear chromosomes is an ongoing process shaped by double-strand-break repair (as shown in yeast) and continuing in humans.

  homo genomic chimpanzee genome genome-wide pcr sanger

• Population history and natural selection shape patterns of genetic variation in 132 genes.

  PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups

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  Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection

  genomic empirical snps chromosome comprehensive coalescent fst

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative

• Interaction profile-based protein classification of death domain.

  PMID 15189571 · PMC459208 · BMC bioinformatics · 2004 · 7 claims · 6 setups

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  An SVM-based classifier using Residue Pair Interaction Profiles (RPIPs) can classify death domain superfamily members into subfamilies with 89% average cross-validation accuracy

  homology-modeled death homology putative rigid-body homology model

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Shiny-Calorie: a context-aware application for indirect calorimetry data analysis and visualization using R.

  PMID 41640623 · PMC12867577 · Bioinformatics advances · 2026 · 8 claims · 8 setups

  Has reproduction · 100

  Shiny-Calorie is an open-source interactive application for transparent data and metadata integration, statistical analysis, and visualization of indirect calorimetry datasets.

  datasets clinical calr imported indirect import physical

• HIV-1 Nef binds the DOCK2-ELMO1 complex to activate rac and inhibit lymphocyte chemotaxis.

  PMID 14737186 · PMC314466 · PLoS biology · 2004 · 8 claims · 8 setups

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  HIV-1 Nef binds the DOCK2-ELMO1 complex (which also contains Rac) in T cells

  jurkat hek resting ns1 two-step ni-nta anti-flag

• Constructing support vector machine ensembles for cancer classification based on proteomic profiling.

  PMID 16689692 · PMC5173238 · Genomics, proteomics & bioinformatics · 2005 · 7 claims · 4 setups

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  CSVME, built by selecting a subset of base SVMs via SVM-RFE ranking and fusing them with a trained upper-layer SVM, achieves better classification performance than an ensemble of all base SVMs.

  serum computational seldi-tof svm-rfe-based 10-fold

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

  PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

  genome functional registered omim comparative kendall's homology

• Gene expression profile of cervical tissue compared to exfoliated cells: impact on biomarker discovery.

  PMID 15876354 · PMC1164412 · BMC genomics · 2005 · 8 claims · 5 setups

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  The gene expression profile of exfoliated cervical cells partially represents that of cervical tissue

  exfoliated normal gene cin3 genome microarray gene

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

  PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

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  Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

  unrelated same snps haplotype snp haplotype pairwise

• Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

  PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog

  chicken predicted human-chicken cdna comparative blastp pairwise

• Towards precise classification of cancers based on robust gene functional expression profiles.

  PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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  Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

  nci60 lymphoma fep go-annotated cdna recursive hypergeometric

• A qualitative assessment of direct-labeled cDNA products prior to microarray analysis.

  PMID 15762992 · PMC1079821 · BMC genomics · 2005 · 5 claims · 5 setups

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  The Agilent 2100 Bioanalyzer can be used in a novel assay to assess the quality/quantity of direct-labeled Cy-dye cDNA prior to microarray hybridization

  mcf-7 same 16lu bioanalyzer agarose cdna

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.

  PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors

  ht1080 coli ht1080-derived synthetic novo gel transposition

• Free energy of DNA duplex formation on short oligonucleotide microarrays.

  PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

  mapping50k_xba240 dgcr hg-u133a pdnn free correlation